thank you sir actually I am student of BS(Hons.) Bionfo & Biotech and Chimera was my presentation topic , Today was my presention and I do alot ..I presented the following1- Introduction to chimera2-How to load a structure into chimera   open  and  fetch3- How to edit, select(chains, residues, atoms, also atom specifier), delete, 4- Actions, zoom and drag , coloring and change the view of model (bonds, atoms, surface, ribbon, residues etc...) 5-How to make animations6-How to use commands7-How to save animation in movie file and in accession file8- How to align and superimpose two or more model structures and then their sequences and how to check RMSD9-How to make or built a structure from peptide or amino acid sequence , and how to get or show the sequnce from protein model10-How to make Ramachandran Plot11-How to save high defination image12-How adjust bonding13-How to make solvate model 14-How to make userinterface of our own choice15-How to select tow different atoms and then how to make bond between them16-How to merg two different model into one17-How to two find a conserved region in the structure by giving the conserved sequence as input19-How to select and activate a specific model20-How to move different objects by mouse 21-How to split a model into its chains22-How to close a specific model23-commands24-How to show the ligand surface25-ViewDock check the binding between the ligand and receptor26-How to check the resolution of PDB structure27-How to measure volume and area28-How to save selected part of model into another separate as a PDB file29-analyzing metal ion coordination geometries30-viewing controls (side view, camera, lighting, shining)31-Find clashes and contacts32-Docking with autodock vina ( ligand-receptor binding )  thank you so much sir for helping...... --- On Tue, 4/9/13, Elaine Meng <meng@cgl.ucsf.edu> wrote: From: Elaine Meng <meng@cgl.ucsf.edu> Subject: building DNA To: "Muhammad ALi" <muh.ali741@yahoo.com> Cc: "chimera-users@cgl.ucsf.edu Mailing List" <chimera-users@cgl.ucsf.edu> Date: Tuesday, April 9, 2013, 4:15 PM On Apr 8, 2013, at 6:42 AM, Muhammad ALi wrote:

hi can we make a DNA model with chimera???

Hello, Although you can build very approximate DNA in Chimera with the "rna" command <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html>, the result is rough and mainly just for viewing.  If you are planning to do detailed modeling or further calculations with the DNA, I would recommend not using Chimera, but instead some other program. For example, here are some web servers that I believe will build DNA: <http://structure.usc.edu/make-na/> <http://w3dna.rutgers.edu/index.php/rebuild> Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

Hi How are you.....Sir I am doing docking with autodock vina in Chimera.. but sir i successfully did it, but with Opal server, and found the required binding sites of ligand binding and checked theier bonds,, but kindly sir tell me  how can i do it without using opal server.. which file will be required???? and how it is estimated that which binding between ligand and protein is best and how???   --- On Tue, 4/9/13, Elaine Meng <meng@cgl.ucsf.edu> wrote: From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] building DNA To: "Muhammad ALi" <muh.ali741@yahoo.com> Cc: "chimera-users@cgl.ucsf.edu Mailing List" <chimera-users@cgl.ucsf.edu> Date: Tuesday, April 9, 2013, 8:25 PM You're welcome!  Wow, you really did a lot! Elaine On Apr 9, 2013, at 12:32 PM, Muhammad ALi wrote:

thank you sir actually I am student of BS(Hons.) Bionfo & Biotech and Chimera was my presentation topic , Today was my presention and I do alot .. I presented the following 1- Introduction to chimera 2-How to load a structure into chimera     open  and  fetch 3- How to edit, select(chains, residues, atoms, also atom specifier), delete, 4- Actions, zoom and drag , coloring and change the view of model (bonds, atoms, surface, ribbon, residues etc...) 5-How to make animations 6-How to use commands 7-How to save animation in movie file and in accession file 8- How to align and superimpose two or more model structures and then their sequences and how to check RMSD 9-How to make or built a structure from peptide or amino acid sequence , and how to get or show the sequnce from protein model 10-How to make Ramachandran Plot 11-How to save high defination image 12-How adjust bonding 13-How to make solvate model 14-How to make userinterface of our own choice 15-How to select tow different atoms and then how to make bond between them 16-How to merg two different model into one 17-How to two find a conserved region in the structure by giving the conserved sequence as input 19-How to select and activate a specific model 20-How to move different objects by mouse 21-How to split a model into its chains 22-How to close a specific model 23-commands 24-How to show the ligand surface 25-ViewDock check the binding between the ligand and receptor 26-How to check the resolution of PDB structure 27-How to measure volume and area 28-How to save selected part of model into another separate as a PDB file 29-analyzing metal ion coordination geometries 30-viewing controls (side view, camera, lighting, shining) 31-Find clashes and contacts 32-Docking with autodock vina ( ligand-receptor binding )

  thank you so much sir for helping......

--- On Tue, 4/9/13, Elaine Meng <meng@cgl.ucsf.edu> wrote:

From: Elaine Meng <meng@cgl.ucsf.edu> Subject: building DNA To: "Muhammad ALi" <muh.ali741@yahoo.com> Cc: "chimera-users@cgl.ucsf.edu Mailing List" <chimera-users@cgl.ucsf.edu> Date: Tuesday, April 9, 2013, 4:15 PM

On Apr 8, 2013, at 6:42 AM, Muhammad ALi wrote:

...

hi can we make a DNA model with chimera???

Hello, Although you can build very approximate DNA in Chimera with the "rna" command <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html>, the result is rough and mainly just for viewing.  If you are planning to do detailed modeling or further calculations with the DNA, I would recommend not using Chimera, but instead some other program.

For example, here are some web servers that I believe will build DNA: <http://structure.usc.edu/make-na/> <http://w3dna.rutgers.edu/index.php/rebuild>

Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Sir when I download a ligand from PDB site it contains may ligand molecules ..and kindly tell me how to get a single ligand???? --- On Thu, 4/11/13, Elaine Meng <meng@cgl.ucsf.edu> wrote: From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Docking To: "Muhammad ALi" <muh.ali741@yahoo.com> Cc: "chimera-users@cgl.ucsf.edu Mailing List" <chimera-users@cgl.ucsf.edu> Date: Thursday, April 11, 2013, 4:24 PM Hello, The Chimera "AutoDock Vina" dialog has a choice: Executable location "Opal web service" or "Local."  To use Local, you would first need to download and install the AutoDock Vina program on your own computer, and then put the location of that executable in the Chimera dialog. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> AutoDock Vina is from a different group (it is not developed by the Chimera team).  You would have to go to the AutoDock Vina website to download the program, and to find more information about how that program works. AutoDock Vina website: <http://vina.scripps.edu/> AutoDock Vina paper: AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Trott O, Olson AJ. J Comput Chem. 2010 Jan 30;31(2):455-61. <http://www.ncbi.nlm.nih.gov/pubmed/19499576> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 11, 2013, at 6:51 AM, Muhammad ALi wrote:

Sir I am doing docking with autodock vina in Chimera.. but sir i successfully did it, but with Opal server, and found the required binding sites of ligand binding and checked theier bonds,, but kindly sir tell me  how can i do it without using opal server.. which file will be required???? and how it is estimated that which binding between ligand and protein is best and how???